kmerLink {FindMyFriends} | R Documentation

## Link gene groups by homology

### Description

This method allows the user to define a secondary grouping of genes be linking gene groups based on sequence similarity (paralogues). A representative for each gene group is used for the calculations and the similarity is assessed using the kmer based cosine similarity.

### Usage

    kmerLink(object, ...)

    ## S4 method for signature 'pgVirtual'
    kmerLink(object, lowMem, kmerSize, lowerLimit, rescale,
      transform, pParam, algorithm, ...)

### Arguments

`object` | A pgVirtual subclass
`...` | parameters passed on to the community detection algorithm.
`lowMem` | logical. Should low memory footprint be ensured over computation speed
`kmerSize` | The size of kmers to use for similarity calculations.
`lowerLimit` | The lower threshold for similarity below which it is set to 0
`rescale` | Should Similarities be normalised between lowerLimit and 1
`transform` | Transformation function to apply to similarities
`pParam` | An optional BiocParallelParam object that defines the workers used for parallelisation.
`algorithm` | The name of the community detection algorithm from igraph to use for gene grouping. See `communities` for an overview. The trailing '.community' can be omitted from the name. Default is 'infomap', which is also the recommended.

### Value

An object with the same class as object with linking between gene groups.

### Methods (by class)

- `pgVirtual`: Linking for pgVirtual subclasses

### Examples

    testPG <- .loadPgExample(withGroups=TRUE)

    # No paralogue links
    hasParalogueLinks(testPG)

    # Create the links
    testPG <- kmerLink(testPG)

[Package FindMyFriends version 1.10.0 Index]